[2024-01-24 13:21:57,521] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:57,523] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:57,523] [INFO] DQC Reference Directory: /var/lib/cwl/stg950efb0e-d5de-4ef3-b82c-9a677fa20c94/dqc_reference
[2024-01-24 13:21:58,836] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:58,837] [INFO] Task started: Prodigal
[2024-01-24 13:21:58,837] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e840d7c-d1e6-467d-bf89-bc9e01ab5a44/GCF_014836875.1_ASM1483687v1_genomic.fna.gz | prodigal -d GCF_014836875.1_ASM1483687v1_genomic.fna/cds.fna -a GCF_014836875.1_ASM1483687v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:09,996] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:09,997] [INFO] Task started: HMMsearch
[2024-01-24 13:22:09,997] [INFO] Running command: hmmsearch --tblout GCF_014836875.1_ASM1483687v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg950efb0e-d5de-4ef3-b82c-9a677fa20c94/dqc_reference/reference_markers.hmm GCF_014836875.1_ASM1483687v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:10,311] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:10,313] [INFO] Found 6/6 markers.
[2024-01-24 13:22:10,346] [INFO] Query marker FASTA was written to GCF_014836875.1_ASM1483687v1_genomic.fna/markers.fasta
[2024-01-24 13:22:10,346] [INFO] Task started: Blastn
[2024-01-24 13:22:10,346] [INFO] Running command: blastn -query GCF_014836875.1_ASM1483687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg950efb0e-d5de-4ef3-b82c-9a677fa20c94/dqc_reference/reference_markers.fasta -out GCF_014836875.1_ASM1483687v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:11,445] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:11,448] [INFO] Selected 9 target genomes.
[2024-01-24 13:22:11,448] [INFO] Target genome list was writen to GCF_014836875.1_ASM1483687v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:11,453] [INFO] Task started: fastANI
[2024-01-24 13:22:11,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e840d7c-d1e6-467d-bf89-bc9e01ab5a44/GCF_014836875.1_ASM1483687v1_genomic.fna.gz --refList GCF_014836875.1_ASM1483687v1_genomic.fna/target_genomes.txt --output GCF_014836875.1_ASM1483687v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:19,448] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:19,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg950efb0e-d5de-4ef3-b82c-9a677fa20c94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:19,448] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg950efb0e-d5de-4ef3-b82c-9a677fa20c94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:19,457] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:19,457] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:19,458] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	100.0	1200	1200	95	conclusive
Arthrobacter gallicola	strain=Sa2CUA1	GCA_014836775.1	2762225	2762225	type	True	90.4842	1056	1200	95	below_threshold
Arthrobacter luteolus	strain=DSM 13067	GCA_008973725.1	98672	98672	type	True	88.9924	1044	1200	95	below_threshold
Arthrobacter luteolus	strain=NBRC 107841	GCA_001552075.1	98672	98672	type	True	88.9729	1035	1200	95	below_threshold
Arthrobacter citreus	strain=DSM 20133	GCA_009192745.1	1670	1670	type	True	82.4887	765	1200	95	below_threshold
Arthrobacter koreensis	strain=DSM 16760	GCA_009193255.1	199136	199136	type	True	82.1054	802	1200	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	80.5429	598	1200	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	80.3232	549	1200	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	80.2913	551	1200	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:19,459] [INFO] DFAST Taxonomy check result was written to GCF_014836875.1_ASM1483687v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:19,460] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:19,460] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:19,460] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg950efb0e-d5de-4ef3-b82c-9a677fa20c94/dqc_reference/checkm_data
[2024-01-24 13:22:19,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:19,501] [INFO] Task started: CheckM
[2024-01-24 13:22:19,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836875.1_ASM1483687v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836875.1_ASM1483687v1_genomic.fna/checkm_input GCF_014836875.1_ASM1483687v1_genomic.fna/checkm_result
[2024-01-24 13:22:55,548] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:55,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:55,572] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:55,573] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:55,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836875.1_ASM1483687v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:55,573] [INFO] Task started: Blastn
[2024-01-24 13:22:55,573] [INFO] Running command: blastn -query GCF_014836875.1_ASM1483687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg950efb0e-d5de-4ef3-b82c-9a677fa20c94/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836875.1_ASM1483687v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:57,327] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:57,331] [INFO] Selected 7 target genomes.
[2024-01-24 13:22:57,332] [INFO] Target genome list was writen to GCF_014836875.1_ASM1483687v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:57,339] [INFO] Task started: fastANI
[2024-01-24 13:22:57,339] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e840d7c-d1e6-467d-bf89-bc9e01ab5a44/GCF_014836875.1_ASM1483687v1_genomic.fna.gz --refList GCF_014836875.1_ASM1483687v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836875.1_ASM1483687v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:03,803] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:03,810] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:03,811] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014836875.1	s__Arthrobacter_B sp014836875	100.0	1200	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014836775.1	s__Arthrobacter_B sp014836775	90.4842	1056	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552075.1	s__Arthrobacter_B luteolus	88.9763	1034	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009192745.1	s__Arthrobacter_B citreus	82.4934	763	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307035.1	s__Arthrobacter_B sp001307035	82.3509	781	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	98.39	98.39	0.92	0.92	2	-
GCF_015355785.1	s__Arthrobacter_B gandavensis_A	82.2167	769	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193255.1	s__Arthrobacter_B koreensis	82.1147	801	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	99.08	99.08	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:03,812] [INFO] GTDB search result was written to GCF_014836875.1_ASM1483687v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:03,812] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:03,815] [INFO] DFAST_QC result json was written to GCF_014836875.1_ASM1483687v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:03,815] [INFO] DFAST_QC completed!
[2024-01-24 13:23:03,815] [INFO] Total running time: 0h1m6s